Atherosclerosis is a multifactorial disease that evolves through complex interactions among lipid metabolism, immune activation, and vascular remodeling. As plaques develop, they may become unstable due to persistent inflammation and structural changes, leading to complications such as plaque rupture and thrombosis. Despite advances in cardiovascular medicine, atherosclerosis remains the leading cause of morbidity and mortality globally, particularly in aging populations. . Disease progression is accompanied by heightened plaque vulnerability, which predisposes individuals to plaque rupture and severe clinical outcomes including heart attack and stroke (1). Despite all the developments in the field of medicine, the pathogenesis of cardiovascular disease still remains multifactorial (2). The condition is marked by the deposition of lipids, inflammatory and smooth muscle cells (SMCs), along with cellular remnants beneath the endothelial layer, leading to notable reductions in vascular blood flow. Decrease in blood flow typically causes angina on exertion or stress. In some patients, unstable plaques may break down and form a blood clot that completely obstructs the coronary arteries and leads to myocardial infarction or a heart attack (3).

The term epigenetics describes heritable changes in gene activity that occur without alterations to the DNA sequence, often through histone modification, and DNA methylation the actions of ncRNAs (4). Epigenetic modifications regulate gene activity independently of changes to the DNA sequence (5) and have emerged as promising biomarkers for cardiovascular disease and therapeutic outcomes. They are influenced by environmental stimuli including as diet, tobacco exposure, and oxidative stress, contributing to sustained alterations in vascular function (6,7). Unlike genetic mutations, epigenetic changes are reversible, making them promising targets for therapy (8).

ncRNAs interact with epigenetic modifiers to fine tune transcriptional programs in vascular cells, influencing inflammation, endothelial dysfunction, and lipid metabolism (9). The three major kinds of ncRNAs are lncRNAs, circRNAs, and miRNAs, each playing distinct roles in gene regulation (10). They influence cellular functions by interacting with RNA, proteins, and DNA to control transcription, translation, and post-transcriptional modifications (11). Among them, miRNAs control gene expression post-transcriptionally by binding to target messenger RNAs (mRNAs), resulting in mRNA degradation or translational repression (12). In the other hand, lncRNAs regulate gene activity through multiple mechanisms, including recruiting chromatin modifiers, acting as molecular scaffolds, or interfering with transcription (13). circRNAs modulate gene regulation by sequestering miRNAs, effectively preventing them from interacting with and repressing their downstream targets (14).

Studies reveal a bidirectional regulatory loop between epigenetic modifications and ncRNAs, suggesting that they work together to establish and sustain pro-atherogenic transcriptional programs (15-19). For instance, lncRNA ANRIL recruits the polycomb repressive complex 2 (PRC2) complex to mediate H3K27 trimethylation, silencing atheroprotective genes, whereas miR-33 represses ATP-binding cassette transporter A1 (ABCA1) expression by enhancing H3K9me3 deposition, impairing cholesterol efflux and promoting the formation foam cells (20,21). However, the full extent of epigenetic-ncRNA crosstalk in atherosclerosis remains poorly understood, particularly in the context of plaque progression and stability. Therefore, this review aimed to examine the interaction between epigenetic modifications and ncRNAs in atherosclerosis, emphasizing their regulatory influence on vascular inflammation, endothelial dysfunction, and plaque progression.

The development of cardiovascular complications in atherosclerosis is associated with an inflammatory process triggered by the deposition of cholesterol-rich lipoproteins within the arterial wall (22). Atherosclerosis develops through a series of interrelated phases, including endothelial dysfunction, lipid deposition, chronic inflammation, plaque development, and eventual plaque rupture (23). Endothelial dysfunction represents the earliest stage of atherosclerosis, often triggered by contributing factors such as hypertension, smoking, high lipid levels, and diabetes. Under normal conditions, the endothelium maintains vascular balance through the inhibition of thrombosis and regulation of vascular tone. However, during dysfunction, it becomes permeable to low-density lipoprotein (LDL) cholesterol, leading to the accumulation of oxidized LDL (oxLDL) in the intimal layer, which triggers an immune response (Fig. 1) (24).

Monocytes in circulation are attracted to the arterial wall following inflammatory stimuli, where they transform into macrophages which play a key role in tissue damage, wound repair, and the regression of plaques (25). This leads to an elevation in the number of M1 macrophages, enhancing the immune response against atherosclerotic fatty streaks. This activation further stimulates the recruitment of additional immune cells and promotes the phagocytosis of platelets and low-density lipoprotein cholesterol (LDL-C). Excessive phagocytosis of LDL results in macrophage death, and the activation of macrophages by specific ligands, coupled with pathogen-induced signaling, facilitates the formation of foam cells (26). The accumulation of foam cells in the shoulders and necrotic core of the plaque leads to the release of metalloproteinases, which contribute to plaque disruption and increased instability (Fig. 2) (27). These macrophages upregulate receptors such as LOX-1 and various transporters, including ABCA1 and ABCG1, which are linked to the suppression of reverse cholesterol transport and the activation of scavenger receptors (28). As the inflammatory process continues, SMCs from the media migrate to the intima, proliferate, and secrete extracellular matrix components, leading to fibrous cap formation over the lipid core. This structure is referred to as an atherosclerotic plaque (29,30). Over time, plaques may grow, leading to luminal narrowing, which can result in ischemic symptoms such as angina. If the fibrous cap weakens due to sustained inflammation, plaque rupture may occur, exposing thrombogenic material and triggering platelet aggregation and clot formation (31). This complex cascade of cellular and molecular events ultimately transforms a protective immune response into a chronic pathological process, driving the progression and clinical manifestations of atherosclerosis.

DNA methylation refers to the process in which a carbon-bound methyl unit is added to the 5′ carbon of cytosine, most commonly within CpG dinucleotides. This modification is crucial for gene silencing, chromatin regulation, and the inheritance of epigenetic traits. This modification, facilitated by DNMTs, plays a crucial role in the regulation of gene expression (32). Methylated DNA attracts methyl-CpG-binding proteins, such as MeCP2, which recruit HDACs and chromatin remodelers. The inactivation of genes through DNA methylation is mediated by methyl-CpG-binding domain (MBD) proteins, which specifically recognize methylated DNA. MeCP2, the first identified protein in this family, depends on its MBD domain for binding. Further studies revealed additional MBD family members (MBD1–MBD4), all of which preferentially bind methylated DNA except MBD3. MeCP2, MBD1, and MBD2 also possess transcription repression domains, enabling gene silencing (33-36). Protein synthesis, or translation, is a tightly controlled mechanism crucial for gene expression. Its disruption has been increasingly associated with various diseases, such as heart-related conditions (37). This process ensures proper gene expression in normal physiological conditions. However, in atherosclerosis, aberrant DNA methylation patterns disrupt this balance, altering the expression of critical genes that affects vascular remodeling, inflammation, lipid metabolism, and endothelial function (38). The capacity of DNA methylation to stably reprogram transcriptional states positions it as a pivotal mechanism linking environmental and metabolic cues to enduring epigenetic alterations in vascular pathology.

Hypermethylation of atheroprotective genes within atherosclerotic plaques contributes to vascular dysfunction by disrupting endothelial homeostasis. The upregulation of DNA methyltransferase 3B (DNMT3B) in response to ox-LDL leads to the epigenetic silencing of key endothelial regulators such as cellular repressor of E1A-stimulated genes (CREG) (39). This repression diminishes nitric oxide bioavailability, impairing endothelial-dependent vasodilation and affecting vascular stiffness (40). Similarly, the hypermethylation of Krüppel-like factor 2 (KLF2), a transcription factor essential for maintaining anti-inflammatory and anti-thrombotic endothelial functions, facilitates endothelial activation and monocyte adhesion, accelerating the progression of atherosclerotic plaque development (41-43). These epigenetic alterations are exacerbated by oxidative stress, which enhances DNMT3B activity and reinforces DNA hypermethylation, thereby sustaining endothelial dysfunction and chronic vascular inflammation (39,44-46). Pharmacological DNMT inhibitors such as 5-aza-2′-deoxycytidine (5-aza-dC) and antioxidants like N-acetylcysteine (NAC) have demonstrated potential in reversing CREG suppression, restoring NO production, and mitigating endothelial dysfunction (39), but face challenges related to delivery and off-target effects (Table I).

Specific promoter methylation events in genes involved in lipid handling, such as ABCA1 and ABCG1, have been linked to impaired cholesterol transport and the progression of atherosclerosis. A human study examining epicardial adipose tissue in patients with coronary artery disease (CAD) identified specific CpG sites within the ABCA1 promoter region, including chr9:107690762, 107690770 (cg14019050), 107690773, 107690791, and 107690797 (GRCh37/hg19), that exhibited significant hypermethylation in CAD patients compared to controls. This site-specific methylation was associated with reduced ABCA1 mRNA and protein expression in epicardial adipose tissue (EAT), particularly in individuals with multifocal atherosclerosis, suggesting that epigenetic silencing of ABCA1 may impair reverse cholesterol transport and promote lipid accumulation in the vascular wall (52). Mechanistically, promoter hypermethylation at ABCA1 recruits methyl-CpG-binding proteins such as MeCP2, which, via interaction with DNMT1 and EZH2, enforces a repressive chromatin structure, including H3K27me3 deposition, thereby silencing ABCA1 transcription and impairing cholesterol efflux in macrophages. This process is further enhanced by the lncRNA GAS5, which binds to EZH2 and recruits it to the ABCA1 promoter to amplify this epigenetic silencing mechanism (53). Additionally, hypermethylation was observed at regulatory CpG sites in the ABCG1 gene, including chr21:43642336 to 43642367 (cg27243685) and chr21:43656587 (cg06500161), in both EAT and subcutaneous adipose tissue. These epigenetic alterations were associated with elevated triglyceride levels, increased body mass index, and reduced ABCG1 expression (52). Another study analyzing leukocyte DNA from men with CAD reported that methylation levels at eight CpG dinucleotides within the ABCA1 promoter region were significantly elevated in older CAD patients. This locus-specific hypermethylation correlated positively with pro-atherogenic lipid markers such as total cholesterol, LDL-C, and triglycerides, suggesting a direct link between promoter methylation and impaired reverse cholesterol transport (54). Together, these findings support the role of ABCA1 and ABCG1 methylation in adipose tissue as a contributing factor to atherosclerosis development through disrupted lipid metabolism and local inflammatory responses. Table II summarizes DNA methylation and lncRNA-mediated chromatin remodeling events affecting lipid transporter expression and downstream atherogenic processes.

DNA methylation also regulates foam cell formation by repressing genes involved in cholesterol efflux (62-64). Hypermethylation of the ABCA1 promoter suppresses its expression, leading to intracellular lipid accumulation. This repression is further reinforced by ncRNAs, such as miR-33, which recruits PRC2 to deposit repressive H3K27me3 marks, thereby sustaining ABCA1 silencing. In addition to its role in silencing ABCA1, miR-33 expression itself is modulated by epigenetic regulation at the SREBP2 locus, where chromatin modifications, including histone acetylation and DNA methylation, influence its transcriptional activity. This reciprocal regulation highlights the dynamic interplay between miR-33 and its epigenetic environment, further linking epigenetic control to cholesterol homeostasis and atherogenesis (65).

ABCA1 expression is regulated by a range of epigenetic mechanisms that influence atherosclerotic progression. These include DNA methylation, histone modifications, and lncRNA-mediated chromatin remodeling. miR-152 and miR-148a indirectly influence methylation through targeting DNMT1, restoring ABCA1 expression and promoting cholesterol efflux (Fig. 3) (66). This adds another layer to the epigenetic regulation of ABCA1, distinct from the miR-33–PRC2 pathway. While miR-33 suppresses ABCA1 through PRC2-mediated histone modification, miR-152/148a operates through methylation, showcasing the complex interplay between miRNA regulation and chromatin modification in atherosclerosis. The results emphasize the contribution of epigenetic regulation to vascular stiffening and lesion formation, identifying DNA methylation as a viable target for therapeutic intervention in atherosclerosis.

Several lncRNAs, such as GAS5 and MeXis, have been shown to either recruit chromatin-modifying complexes or interact directly with epigenetic regulators that modulate ABCA1 transcription. Dysregulation of these pathways has been associated with impaired cholesterol efflux, macrophage foam cell formation, and plaque development, highlighting the importance of epigenetic control of ABCA1 in atherosclerosis (67). Notably, several lncRNAs that regulate chromatin architecture at lipid-handling gene loci are themselves subject to epigenetic regulation. For example, histone acetylation can enhance MeXis transcription, which in turn promotes ABCA1 expression by facilitating LXR-driven activation (67,68). This illustrates a bidirectional regulatory loop in which epigenetic marks modulate ncRNA activity, and ncRNAs reciprocally shape the epigenetic landscape at key atherosclerosis-related genes.

Histone modifications serve as pivotal regulators of gene expression by reshaping chromatin structure and modulating DNA accessibility. These dynamic chemical changes, such as acetylation, methylation, phosphorylation, and ubiquitination, are catalyzed by specialized enzymes: histone acetyltransferases (HATs), which add acetyl groups to promote transcription; HDACs, which remove acetyl groups to repress gene activity; histone methyltransferases (HMTs), which transfer methyl groups to histone tails and influence gene activation or repression depending on the site; and histone demethylases (HDMs), which remove methyl groups to reverse these effects (19). Aberrant histone modifications play a key role in endothelial dysfunction, chronic inflammation, and plaque instability (69,70).

Several studies have shown that DNA methylation and histone modifications are closely interrelated, functioning in a coordinated and locus-specific manner to regulate gene expression in atherosclerosis. Specific patterns of these epigenetic marks have been identified at promoters of key vascular genes involved in inflammation, lipid metabolism, and endothelial function (62). For example, the NOS3 (eNOS) promoter displays hypermethylation and reduced H3K27ac and H3K4me3, contributing to endothelial dysfunction by silencing nitric oxide synthesis genes (71). In contrast, the IL6 promoter exhibits increased H3K4me3 enrichment in oxLDL-trained monocytes, which contributes to sustained pro-inflammatory gene expression in macrophages (72,73).

The interplay between histone modifications and ncRNAs further modulates transcriptional programs in vascular cells, contributing to endothelial dysfunction, foam cell formation, and plaque progression (74). Through their coordination with non-coding RNAs and chromatin-modifying enzymes, histone modifications establish a dynamic epigenetic landscape that governs vascular cell behavior and promotes the epigenetic reprogramming underlying atherogenesis. The following sections will explore these histone modifications in greater detail, highlighting their site-specific effects, interacting partners, and implications in vascular pathology.

In histone methylation, a methyl donor, S-adenosyl-L-methionine, transfers a methyl group to arginine or lysine residues on histone tails, thereby modulating gene expression. Notably, this modification process does not affect the histone protein charge (75). This modification results in mono-, di-, or trimethylation (me1, me2, me3) of particular histone amino acids, influencing gene activity without altering the DNA sequence. Histone methylation has important roles in the establishment of heterochromatin, gene imprinting, transcriptional regulation, and X-chromosome inactivation (76).

The interaction between histone methylation and noncoding RNAs has been widely studied. LncRNAs control histone methylation by engaging with methyltransferases, demethylases, or complexes like PRC2 which play a role in chromatin modification, while miRNAs influence the process by targeting the mRNAs of related proteins (4,77). Histone modifications, including methylation and HDAC overexpression, also regulate miRNAs and lncRNAs. Proteins and enzymatic complexes responsible for histone modifications can be directed to the promoters of ncRNA genes, resulting in either upregulation or silencing of their transcription (78). An animal study found that miR-126-5p is essential for EC replication after injury by targeting Dlk1, a suppressor of proliferation. This mechanism supports endothelial repair under hyperlipidemic stress and reduces lesion formation in atherosclerosis-resistant arteries. Conversely, disturbed flow lowers miR-126-5p levels, weakening endothelial proliferation at vulnerable sites and increasing susceptibility to atherosclerosis (79).

Well known lysine methylation sites include H3(K4, K9, K27, K36, K79, and K20), whereas arginine methylation occurs at H3(R2, R8, R17, R26, and R315). The effect of histone methylation on transcription is site specific. Methylation at H3(K4, K36, K79, and R17) is associated with transcriptionally active regions, whereas H3(K9, K27, and K20) are linked to transcriptionally repressed regions (80).

H3K4me3 is one of the most extensively studied histone marks due to its presence at transcription start sites and its strong correlation with active gene expression, cellular differentiation, development, and disease progression (81), including its involvement in the progression and severity of atherosclerosis (82). In endothelial cells, the presence of H3K4me3 at the vascular endothelial growth factor receptor 2 (VEGFR2) promoter enhances its expression, promoting endothelial proliferation and angiogenesis (83). This process is critically influenced by miR-126-5p, an endothelial-enriched miRNA (84) that has been shown to facilitate the recruitment of SET1A/MLL1 (85), a major H3K4 methyltransferase, to the VEGFR2 promoter, thereby reinforcing the transcriptional program necessary for endothelial homeostasis.

H3K27 trimethylation (H3K27me3) serves as a potent transcriptional silencing mechanism that contributes to the repression of anti-inflammatory and anti-proliferative genes in vascular cells (86). One of the most well-studied ncRNAs involved in this regulatory axis is lncRNA ANRIL, which has been implicated in atherogenesis through its interactions with PRC2 (87-89). As a structural platform, ANRIL supports the localization of enhancer of zeste homolog 2 (EZH2), the active subunit of thePRC2 (90), to the promoters of atheroprotective genes such as CDKN2A/B, thereby enforcing their repression through H3K27me3 deposition (91). Given that CDKN2A/B encodes key cell cycle inhibitors that regulate VSMC apoptosis and proliferation, its silencing by ANRIL promotes excessive VSMC proliferation, a hallmark of atherosclerotic plaque development (92). Early atherogenesis is associated with elevated acetylation of H3K9 and H3K27 across the genome, whereas late atherogenesis involves increased methylation of H3K4 and H3K9(82). During atherogenesis, H3K27Me3 levels decrease in vascular SMCs (VSMCs) while increasing in endothelial cells, indicating cell-specific epigenetic regulation despite a shared extracellular environment (93). Clinical studies have reported that ANRIL expression is highly upregulated in advanced human atherosclerotic plaques, and its expression correlates with increased PRC2 occupancy and H3K27me3 (88,94,95). Notably, ANRIL expression itself is also subject to epigenetic regulation. Chromatin accessibility at the 9p21 locus, where ANRIL is encoded, is modulated by local histone modifications and DNA methylation patterns, forming a feedback loop in which ANRIL both responds to and shapes the epigenetic environment (87,96). These findings suggest that targeting the ANRIL-PRC2 axis is a potential therapeutic target to modulate histone methylation and restore the normal expression of protective genes in vascular cells.

Histone modifications, particularly those mediated by lysine-specific demethylase 1A (KDM1A), play an important regulatory effect in plaque instability and progression (97). For instance, the interaction between lnc_000048 and KDM1A reduces histone demethylase activity, activating MAP2K2 and ERK phosphorylation, which amplifies inflammation through the MAPK pathway. ApoE−/− mice studies confirm that lnc_000048 promotes inflammatory responses and degradation of collagen, further linking histone methylation to atherosclerosis progression (98). Together, these findings highlight histone methylation as a context-dependent regulator of vascular cell phenotype and plaque dynamics, with emerging implications for targeted epigenetic therapy in atherosclerosis.

Histone acetylation is a key epigenetic mechanism that modulates gene expression by loosening chromatin structure and enhancing DNA accessibility (99). In eukaryotic cells, histone acetylation serves as a key epigenetic mechanism that influences chromatin organization and transcriptional activity, thereby regulating gene expression. This process play a key role in controlling cell cycle progression and cellular differentiation. This modification involves adding an acetyl group to lysine amino acids located along the extended tails of histone proteins, typically resulting in a relaxed chromatin structure that supports transcription (100). In atherosclerosis, HDAC overexpression has been linked to vascular inflammation and foam cell formation. HDAC9, in particular, suppresses atheroprotective genes and enhances NF-κB-driven pro-inflammatory responses, accelerating lesion formation (101). The impact of HDACs on chromatin structure and inflammatory signaling highlight the broader role of histone acetylation in shaping the transcriptional landscape of vascular cells during atherogenesis.

The enzymatic function of HATs involves sourcing acetyl groups from acetyl-CoA, which are then delivered to lysine residues along histone tail regions, altering chromatin accessibility. As glucose serves as a key substrate for acetyl-CoA synthesis via the tricarboxylic acid cycle, fluctuations in its levels can impact the availability of acetyl groups, thereby modulating histone acetylation (102,103). It has been proposed that 37 mammalian proteins have intrinsic HAT activity, classified into five major subfamilies based on structural similarities. These categories include GCN5/PCAF, MYST, CBP/p300, nuclear receptor coactivators, as well as basal transcription factor families (104).

Evidence indicates that core histone acetylation plays a role in various cardiovascular disorders, including hypertension, diabetic cardiomyopathy, and myocardial infarction. It also play an important role in cellular dysfunctions like excessive VSMCs growth and programmed cell death (105). Histone acetylation at inflammatory gene promoters has been linked to endothelial dysfunction (62,104). Interestingly, Impairment of vascular endothelial cells is regarded as a key player in the early phase of atherosclerotic progression (106). Atherosclerosis begins with endothelial cell activation, disrupting their role in hemostasis, vascular tone, and inflammation. This dysfunction triggers disease progression, allowing circulating monocytes to penetrate the endothelium and infiltrate both the intimal and subintimal regions (62). The expression and release of cytokines in infectious diseases are influenced by histone acetylation. In dengue virus-infected monocytes, endothelial cells, and epithelial cells, IL-8 secretion increases, causing a notable elevation in its serum concentration (104). During macrophage differentiation, cells shift from an anti-inflammatory M2 state to a proinflammatory M1 phenotype. PPAR-γ regulates this process, with epigenetic mechanisms playing a role. In an atherosclerosis mouse model, macrophage-specific DNMT1 overexpression increased proinflammatory cytokines and accelerated disease progression (107). The role of histone acetylation in promoting endothelial dysfunction, inflammatory cytokine release, and macrophage-mediated immune activation highlights its direct contribution to the early cellular events driving atherosclerosis.

ncRNAs play are key regulators of histone acetylation, shaping gene expression patterns and contributing to the progression of atherosclerosis (108). For example, The long non-coding RNA Kcnq1ot1 promotes atherosclerosis by upregulating HDAC3, which suppresses ABCA1, impairs cholesterol efflux, and drives lipid accumulation. Acting as a competing endogenous RNA (ceRNA), it binds to miR-452-3p, preventing HDAC3 repression and exacerbating foam cell formation. In contrast, Kcnq1ot1 knockdown reduces plaque formation and enhances cholesterol efflux, highlighting its therapeutic potential (109). lncRNA MANTIS also associates with SWI/SNF, a chromatin-remodeling complex, to enhance H3K27 acetylation at protective endothelial gene sites and maintain vascular stability (110).

HDACs remove acetyl groups from lysine, condensing chromatin and repressing gene expression. They belong to HDAC and sirtuin families, consisting of 18 members categorized into four groups: Core Regulators, Structural Modifiers, Metabolic Integrators, and Multifunctional Enzymes (111). The involvement of HDACs in atherosclerosis stems from their role in controlling various metabolic and cellular processes essential to disease progression. They influence glucose and lipid metabolism, control endothelial cell activation and dysfunction, and impact foam cell formation from both macrophages and VSMCs. Additionally, HDACs contribute to VSMC phenotype switching, affecting plaque stability, while also playing a role in plaque rupture and thrombosis (112). For example, several animal studies reported that HDAC3, and HDAC9 influences macrophage behavior in atherosclerotic plaques. HDAC3 deletion in mice led to enhanced collagen deposition, promoting plaque stability (113,114). HDAC3 supports endothelial function, regulates VSMCs proliferation and migration, influences macrophage polarization, and impacts foam cell development (115). These interconnected regulatory layers underscore the central role of histone acetylation and its modulators in orchestrating vascular cell behavior, immune responses, and lipid handling, thereby integrating epigenetic control into the core mechanisms driving atherosclerotic progression.

Studies indicate that HDACs are key regulators of oxidative stress and inflammation. Researchers observed that in conditions of disturbed blood flow, HDAC2, HDAC3, and HDAC5 expression increased in the rat aortic arch, contributing to a pro-atherogenic endothelial phenotype (116). HDAC1 and HDAC inhibitors (HDACi) regulate antioxidant enzymes such as CAT and SOD, which neutralize superoxide both in vivo and in vitro (117). Exposure of endothelial cells to ox-LDL increases HDAC6 expression and activity, which in turn lowers cystathionine γ-lyase levels and promotes endothelial dysfunction (118). CircRSF1 regulates ox-LDL-induced endothelial cell proliferation, apoptosis, and inflammation in atherosclerosis via the miR-135b-5p/HDAC1 pathway, offering novel insights into potential diagnostic and therapeutic strategies (119). In an animal study, Tian et al (120). demonstrated that YY1/HDAC2/miR-155/HBP1 axis contributes to macrophage-derived foam cell generation in the initial phases of atherosclerosis, highlighting the therapeutic potential of miR-155. These results suggest that HDACs are key regulators of inflammation, oxidative stress, and endothelial dysfunction in atherosclerosis. Their involvement in endothelial cell regulation and foam cell formation highlights their potential as therapeutic targets.

Endothelial-to-mesenchymal transition (EndMT) is a cellular process where endothelial cells adopt mesenchymal features, acquiring traits similar to myofibroblasts or SMCs. Growing evidence suggests that EndMT involvement in cardiovascular diseases, including atherosclerosis (121). An animal study revealed that EndMT is linked to the deacetylation of key histone residues, highlighting the role of histone modifiers in its regulation. Furthermore, the study demonstrated that inhibiting HDACs belonging to class IIa can suppress EndMT both in vitro and in vivo, with HDAC9 identified as the principal isoform driving this transition (122). HDAC9 knockdown via specific shRNA effectively mitigated endothelial apoptosis triggered by ox-LDL and reduced the expression of inflammatory markers, including TNF-α and MCP1, highlighting HDAC9's pivotal role in mediating vascular inflammation and dysfunction (123). Interestingly, miR-182 promotes atherogenesis in ApoE-knockout mice by regulating HDAC9, which in turn increases lipoprotein lipase expression, enhances lipid accumulation, and stimulates proinflammatory cytokine production in atherosclerotic lesions (124). A human study reported that circular RNA hsa_circ_0001879 is upregulated in atherosclerosis and inhibits and inhibits endothelial proliferation and migration by acting as a sponge for miR-6873-5p. This interaction prevents miR-6873-5p-mediated HDAC9 mRNA degradation, sustaining HDAC9 expression (125). Suggesting that hsa_circ_0001879 regulates endothelial dysfunction via an ncRNA-HDAC9 axis, linking circRNAs to epigenetic regulation in atherosclerosis.

Chromatin remodeling is an important epigenetic process that dynamically alters nucleosome positioning, thereby regulating gene expression in response to environmental stimuli (126). Nucleosomes play a key role in organizing and protecting genomic DNA, ensuring proper cellular function and development in eukaryotic organisms. Although nucleosomes have some structural flexibility, their arrangement is primarily controlled by ATP-dependent chromatin remodelers (127). These remoders such as the sucrose nonfermenting-type (SWI/SNF) complexes, are multiprotein assemblies that modify chromatin structure, thereby regulating the accessibility of genomic DNA to key regulatory proteins, including transcription factors (TFs) (128). These SWI/SNF complexes are highly conserved across eukaryotic species. In humans, the primary subtypes of SWI/SNF complexes include polybromo (pBAF), canonical (cBAF), and noncanonical (ncBAF). In Arabidopsis, the functional equivalents of the SWI/SNF complex are SYD-associated SWI/SNF (SAS), MINU-associated SWI/SNF (MAS), and BRAHMA-associated SWI/SNF (BAS) (129,130). The SWI/SNF complex, particularly BRG1, enhances the transcription of pro-inflammatory cytokines by facilitating NF-κB binding at promoters of genes like IL-6 and TNF-α (131). Liao J et al (132) reported that SWI/SNF chromatin remodelers play a pivotal role in determining and activating enhancers during inflammation. Their disruption decreases chromatin accessibility and H3K27ac at lipid A-responsive sites, hindering inflammatory gene transcription. Variants of SWI/SNF show distinct but interdependent functions, with cBAF binding associated with chromatin accessibility changes. This suggests that SWI/SNF variants collaborate to regulate chromatin remodeling. Epigenetic regulation plays an important regulatory role in endothelial function, as demonstrated by the long noncoding RNA MANTIS (133). The expression of this gene is regulated by the histone demethylase JARID1B and fluctuates in response to varying vascular environments. This relationship exemplifies a bidirectional regulatory circuit between ncRNAs and epigenetic machinery. While MANTIS expression is epigenetically controlled, it also modulates chromatin structure by scaffolding BRG1, the ATPase subunit of the SWI/SNF chromatin remodeling complex (60,134). Mechanistically, MANTIS stabilizes BRG1 in its active conformation, thereby enabling its efficient recruitment to the promoter regions of endothelial-specific genes such as SMAD6, COUP-TFII, and SOX18. This interaction enhances chromatin accessibility at these loci, facilitating their transcription and promoting endothelial alignment and angiogenic sprouting under flow conditions. In contrast, depletion of MANTIS impairs BRG1 function, leading to reduced expression of these key genes and compromised vascular regeneration (60,135). These findings highlight the interplay between lncRNAs and chromatin remodeling in gene regulation.

The dynamic relationship between different epigenetic regulators suggests that noncoding RNAs and chromatin remodeling systems influence each other (136,137). The chromatin-associated lncRNA JPX contributes to VSMC senescence and vascular inflammation by scaffolding a transcriptional complex involving phosphorylated BRD4 and p65. In this context, BRD4 functions as a reader of acetylated histones, anchoring the complex to chromatin at promoters of senescence-associated secretory phenotype (SASP) genes such as IL1A and IL6. JPX facilitates the recruitment and stability of this complex, promoting inflammatory gene expression and thereby accelerating atherosclerosis progression. JPX plays an essential role in this complex, but its expression is governed by epigenetic factors, particularly histone modifications at the 9p21 locus, to maintain proper feedback regulation of endothelial inflammation and atherosclerosis (138-140). lncRNA MANTIS has also been implicated in the regulation of angiogenesis through its association with components of the SWI/SNF complex. Notably, this lncRNA is upregulated in the carotid arteries of monkeys on a regression diet for atherosclerosis and in glioblastoma, yet downregulated in pulmonary hypertension (60). Deletion of MANTIS disrupts endothelial cell alignment and impairs angiogenic sprouting under shear stress, further demonstrating its crucial role in modulating angiogenesis through chromatin remodeling (60). These interactions illustrate how noncoding RNAs function not only as downstream targets but also as active modulators of chromatin remodeling complexes, establishing reciprocal regulatory networks that fine-tune vascular gene expression and influence atherosclerotic disease trajectories.

The progression of atherosclerosis involves distinct phenotypic transitions in vascular cells, driven by complex interactions between epigenetic modifications and ncRNAs (141). These regulatory mechanisms influence early endothelial dysfunction, macrophage-driven inflammation, and advanced plaque instability, shaping disease severity and clinical outcomes (142). At the initial stages of atherosclerosis, pro-inflammatory stimuli (ox-LDL, disturbed flow) trigger DNA methylation and histone modifications, leading to endothelial activation. In addition to CREG silencing, DNMT3B also hypermethylates promoters of other endothelial-protective genes such as KLF2 and eNOS, thereby amplifying vascular inflammation and dysfunction (143,144). Hypermethylation across the genome can deactivate protective genes, cause gene mutations, and lead to allelic loss. DNA methylation is driven by DNMTs (DNMT1, DNMT3A, and DNMT3B), while TET proteins (TET1, TET2, and TET3) play a role in reversing this process, ensuring a balanced epigenetic state over time (38).

Macrophage immunometabolism, which refers to the shifts in intracellular metabolic processes that modulate the function of these adaptable cells, has become a major research focus due to its significant roles in atherosclerosis and various inflammatory diseases (145). Macrophage plasticity is regulated by epigenetic mechanisms, with noncoding RNAs (ncRNAs) playing a key role (146). miR-145 overexpression in VSMCs contributes to diminished atherosclerotic plaque burden in regions commonly affected, such as the aortic root, ascending aorta, and brachiocephalic trunk. It also improves plaque stability by elevating VSMC density, collagen levels, and fibrous cap size, and by reducing macrophage presence and necrosis (147). Atherosclerotic plaques are rich in macrophages, which play a central role in driving disease progression. A study investigated the histology of murine atherosclerotic lesions under varying shear stress conditions found that macrophage phenotype is influenced by fluid dynamics. Macrophages subjected to low or truncated shear stress exhibited increased expression of M1-associated inflammatory markers, while oscillatory shear stress favored a shift toward an M2-like phenotype in the affected areas (148). miRNAs, small ncRNAs, regulate various aspects of vascular biology and contribute to the development of atherosclerosis by post-transcriptionally modulating gene expression. This regulatory mechanism has been widely investigated (149).

Monocytes/macrophages and VSMCs in the intima absorb modified LDLs through scavenger receptors and LDLR, contributing to foam cell formation and VSMC activation. miRNAs such as miR-155 (150) and miR-125a-5p (151) regulate lipid uptake and inflammation in monocytes/macrophages. As a result, the buildup of foam cells and fatty streaks in the neointima can be diminished, thereby mitigating plaque development and instability (147).

In endothelial cells, miR-126 plays a critical role in regulating vascular homeostasis by modulating genes including VEGFR2 (152). miR-126 regulates vascular homeostasis in endothelial cells by inhibiting excessive angiogenesis, maintaining a quiescent endothelial phenotype, and reducing endothelial cell proliferation and migration (153). These actions help preserve vascular integrity and have atheroprotective effects, contributing to vascular repair and neovessel formation in response to vascular injury. Epigenetic modifications, such as histone acetylation and DNA methylation, significantly influence endothelial cell function. For instance, hypermethylation of the KLF2 promoter suppresses its expression, contributing to endothelial dysfunction and atherosclerosis (154). Disturbed blood flow enhances the activity of DNMTs, leading to KLF2 silencing (155). On the other hand, laminar shear stress promotes KLF2 expression through histone acetylation and the recruitment of transcriptional co-activators, such as p300, which facilitates KLF2 binding to the promoters of eNOS and other protective endothelial genes (154). Disruption of this epigenetic regulation contributes to the onset of atherosclerosis by impairing vascular function and promoting inflammation.

Moreover, homocysteine (Hcy), a well-known risk factor for atherosclerosis, can induce vascular smooth muscle cell (VSMC) proliferation through epigenetic regulation. Hcy downregulates miR-125b, which leads to the upregulation of DNMT3b, resulting in hypermethylation of the p53 promoter. This suppresses p53 expression, promoting VSMC proliferation and contributing to plaque formation. The miR-125b-DNMT3b-p53 signaling axis underscores the role of epigenetic modifications in VSMC behavior during atherosclerosis progression (156). Similarly, Hcy also regulates miR-143 levels, which modulate DNMT3a expression, contributing further to VSMC proliferation and atherosclerotic plaque development (157). Therefore, targeting the miR-125b-DNMT3b-p53 axis and miR-143-DNMT3a pathway in VSMCs could reverse epigenetic silencing of p53 and KLF2, potentially restoring vascular function and reducing plaque formation.

As aforementioned, miR-33-mediated recruitment of PRC2 to the ABCA1 promoter exemplifies how ncRNAs (158,159), and epigenetic modifiers cooperate to repress cholesterol efflux genes (160), thereby promoting foam cell formation and atherosclerotic plaque progression (61). lncRNA MeXis promotes cholesterol efflux in macrophages by enhancing the transcription of ABCA1. Mechanistically, MeXis functions as a coactivator by recruiting the RNA helicase DDX17, which in turn stabilizes liver X receptor (LXR) binding to the ABCA1 promoter. This interaction facilitates open chromatin conformation and promotes ABCA1 transcription, thereby supporting reverse cholesterol transport and exerting an atheroprotective effect (Fig. 4) (58). Collectively, these findings reveal that the epigenetic regulation of vascular cells is not merely a downstream consequence but a central, instructive force in atherogenesis integrating environmental stimuli with gene expression programs that determine cellular behavior, plaque evolution, and disease outcome.

The growing understanding of epigenetic regulation and ncRNA involvement in atherosclerosis has opened new avenues for therapeutic intervention. Current treatments for atherosclerosis, including statins and antiplatelet therapies, are the cornerstone of clinical management. These therapies have been proven to reduce cholesterol levels and inhibit platelet aggregation, helping to manage the disease and prevent complications (161). By targeting these molecular mechanisms, it is possible to modulate the progression of cardiovascular disease at a molecular level (162). However, translating these advances into therapeutic interventions remains difficult due to unresolved challenges in specificity, delivery methods, and off-target activity.

The reversibility of epigenetic modifications, such as DNA methylation and histone acetylation, makes them attractive for therapeutic use. However, the application of DNMT inhibitors like 5-aza-2′-deoxycytidine (5-aza-dC) has shown limited success in human-like models due to off-target effects and challenges in translating preclinical results to human therapies. In a study using 5-azacytidine (Aza) in ApoE−/− mice, the drug induced the differentiation of naive CD4+ T cells into regulatory T cells (Tregs) by inhibiting DNMTs (Dnmt1, Dnmt3a, Dnmt3b). However, Aza's broad demethylating effect may also impact genes beyond the Foxp3 locus, potentially altering immune function and contributing to unintended inflammatory responses (51). These off-target effects highlight the challenge of achieving specificity in epigenetic therapies, as the widespread influence on DNA methylation could complicate its use in atherosclerosis treatment. Furthermore, in a human study focusing on dendritic cells (DCs), 5-azacytidine altered cytokine secretion profiles, inducing a Th17 immune response characterized by increased production of IL-17A and IL-21, while decreasing IL-4-secreting T cells (163). This suggests that 5-azacytidine could have broader immune-modulating effects, potentially leading to autoimmune manifestations as a side effect of its intended epigenetic changes.

Translating preclinical findings from animal models to human patients remains a significant challenge due to species-specific differences in gene regulation and disease progression. A recent preclinical study on miR-33a-3p inhibition in pro-inflammatory endothelial cells (iMAECs) failed to replicate the atheroprotective effects seen with miR-33a-5p inhibition. Although ABCA1 mRNA levels increased, ABCA1 protein expression and cholesterol efflux did not show significant improvement (50). This emphasizes that therapies successful in animal models may not produce the same outcomes in humans, highlighting the challenges in translating preclinical findings into clinical applications.

Moreover, epigenetic alterations can occur before disease onset, offering potential as diagnostic and prognostic biomarkers for disease risk and progression (164). For example, aberrant DNA methylation at the promoter regions of endothelial-specific genes such as KLF2 and endothelial nitric oxide synthase (eNOS) has been detected in early atherogenic settings, even before macroscopic plaque development. These epigenetic modifications suppress the transcription of KLF2 and eNOS, both of which are critical for maintaining vascular homeostasis through anti-inflammatory, anti-thrombotic, and vasodilatory functions. The resulting decrease in nitric oxide bioavailability and endothelial resilience marks an early shift toward vascular dysfunction and a pro-atherogenic phenotype, suggesting that such methylation patterns may serve as predictive epigenetic biomarkers for subclinical atherosclerosis (143,165). Notably, these changes have been observed in atherosclerosis-prone regions of arteries in ApoE−/− mice and are detectable prior to histological plaque formation, emphasizing their potential utility as early biomarkers (166). However, their application is limited by tissue accessibility and the need for cell-type-specific resolution, as these signatures may not be reflected in circulating cells (167). Furthermore, common risk factors such as diabetes and hypertension can exacerbate epigenetic modifications in endothelial cells, potentially altering the effectiveness of epigenetic therapies (168). These conditions may influence the expression of genes like ABCA1 and eNOS (56), highlighting the need to consider individual genetic backgrounds and environmental factors in the design of epigenetic-based treatments.

ncRNAs are increasingly recognized as potential biomarkers and therapeutic targets in atherosclerosis and vascular dysfunction. However, the cellular and extracellular environments present significant challenges for their targeted delivery and regulatory control. Problems related to specificity, delivery, and tolerance continue to impede the clinical translation of ncRNA-based treatments (169). miRNA-based therapies hold significant promise for atherosclerosis treatment, with miRNA mimics and inhibitors being developed to regulate key pathways in the disease. Anti-miR-33 oligonucleotides, for example, have shown potential in increasing cholesterol efflux and reducing plaque size in animal models (170). However, challenges remain in delivering these therapies to vascular tissues, as systemic delivery often targets the liver and kidneys more efficiently. Additionally, the long-term safety and efficacy of these treatments in atherosclerosis are still under investigation, with the need for improved targeting strategies to maximize therapeutic outcomes (171).

Although promising advancements in ncRNA- and epigenetic-based therapies have been made, translating these therapies into clinical practice is still a work in progress. Challenges related to tissue-specific delivery, long-term toxicity, and disease variability across patient populations need to be addressed. Meanwhile, standard therapies, such as statins and antiplatelet therapies, remain essential in managing atherosclerosis, and ongoing research will be critical to refining novel approaches, improving targeting, and enhancing therapeutic efficacy. Future work needs to address better understanding the bidirectional relationship between ncRNAs and epigenetics in the pathogenesis of atherosclerosis. Investigation into stage-specific molecular signatures and the potential use of combination therapies may lead to more successful and personalized treatments. Identifying novel biomarkers for early detection and therapeutic monitoring will be essential for advancing precision medicine approaches in atherosclerosis management.